The discovery of chemokine receptors as co-receptors for HIV-1 fusion and entry has raised critical questions in the pathogenesis of HIV encepahlopathy. Such questions include the role of CXCR4, which is widely expressed on microglia, macrophages and neurons in the CNS and can mediate viral entry but also functional and neurotoxic effects of the HIV-1 envelope glycoprotein. Other receptors include CCR3, CX3CR1, the cytomegalovirus receptor US28 and APJ. All are highly expressed in mainly on sequences, clones or isolates from CSF or brain tissue. However, CSF variants may not reflect those in parenchyma, and viral species isolated from tissue may not reflect minority variants or can be distinguished from those contaminating the brain from blood cells. Such limitations are an important gap in the understanding of how viruses in vivo interact with chemokine viral co-receptors and how these interactions, suggested by in vitro or non-human animal models, contribute to pathogenesis. The hypothesis being tested is that HIV-1-co-receptor interactions are important in viral compartmentalization and in the pathogenesis in HIV-1 encephalitis (HIVE). In addition, an important role in viral neuropathogenesis may be played by viral variants that are minority species present in specific cells in brain or that that replicate poorly in culture. In this work a novel approach that enables the cloning of viral sequences from individual infected cells in brain using single-cell PCR will be employed. The goals are to define at the individual cell level chemokine receptor interactions of HIV-1 species in brain during HIVE. Specifically the investigators will: (1) Amplify HIV-1 env from individual cells in HIVE autopsy brain and construct functional clones for cell-specific viral analysis: (2) define the use of major, minor and CD4-independent co-receptors by these functional envs: (3) determine their target cell tropism and replication characteristics using pseudotype and recombinant infectious viruses, and (4) use single cell-derived cDNAs to define cell-specific patterns of altered cellular gene expression in infected versus uninfected microglia in brain tissue from HIVE